Alignments for a candidate for gdhA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Sinorhizobium meliloti 1021

Align Glutamate dehydrogenase; EC 1.4.1.2 (characterized, see rationale)
to candidate SMc04085 SMc04085 hypothetical protein

Query= uniprot:G8AE86
         (1618 letters)



>FitnessBrowser__Smeli:SMc04085
          Length = 1595

 Score = 1174 bits (3037), Expect = 0.0
 Identities = 674/1534 (43%), Positives = 900/1534 (58%), Gaps = 38/1534 (2%)

Query: 95   TVVEIVNDDMPFLVDSVTAELNRQGLTVHLVIHPVVRVKRDADGQLAELYEPAAAPTDAA 154
            +++ I   +MPFL DSV  E+      +HL IHP++ ++    G+  +L++P     ++A
Sbjct: 87   SIIAITERNMPFLYDSVMGEVTSTHRDIHLAIHPILVME---PGKPVKLFDP---DEESA 140

Query: 155  PE---SFMHVEVGAVTGAAALDQAREGLERVLADVRAAVADWRAMRQQVRAAIVEADCAR 211
            PE   S + + +  +T   A   ++  +  VL  V  AV DW AM   +  A+ E +   
Sbjct: 141  PEHRVSHIQIHLSRLTPLEARSLSKR-ISDVLEQVHQAVHDWPAMTALLDQAMRELEDYN 199

Query: 212  AAVPAIIPDDEVDEAKAFLSWADDDHFTFLGYREYRFESGADGADSSLGLVAGSGLGILR 271
            A+        + DEA AFL W  D +FTFLG REY +      A    G   G GLGIL 
Sbjct: 200  ASRKK----SDRDEALAFLRWLRDSNFTFLGMREYTYSGKGGRATVERG--KGRGLGILS 253

Query: 272  DDSVTVFDGLRNYATLPPDVRDFLRNPRVLMVTKGNRPSPVHRAVPMDAFLIKRFDAEGR 331
            +  V V    ++     P++  FL  P  L+VTK N  S VHR   MD   IKRFDA G 
Sbjct: 254  NPDVRVLRQGKDAVLTTPEILAFLEGPDFLIVTKANVKSVVHRRAHMDYIGIKRFDASGN 313

Query: 332  IIGERLVAGLFTSVAYNRSPREIPYLRRKVAEVMELAGFDPQGHDGKALLHILETYPRDE 391
            ++GE  + GLFTS AY R   EIP LR K+ ++++  G+DPQ H GK L + LE YPRD+
Sbjct: 314  VVGELRIVGLFTSTAYTRQASEIPLLRHKIEKIVDHFGYDPQSHSGKTLANTLEAYPRDD 373

Query: 392  LFQIQVPELLDIAVGILHLQERQRLALFVRKDPFERFASCLVYVPRDRYDTTLRRRIQSI 451
            LFQI V  L      I  L +R R+ +  R D F+RF S +V+VPR++YD+ +R +I   
Sbjct: 374  LFQIDVGLLAAFCEQINELGDRPRVRVLPRIDHFDRFVSVIVFVPREQYDSDVREKIGDY 433

Query: 452  LEAAYDGTCTGFTTQLTESVLARLHFIIRTEPGRVPTVDATDLEARLVQASRGWDDHLRD 511
            L+  YDG  + +     E  LAR+HFII    G+ P V    LE  +      W D   +
Sbjct: 434  LKTVYDGRVSAYYPAFPEGGLARVHFIIGRSGGKTPRVPQAKLEEAVRAIVTRWIDRF-N 492

Query: 512  ALVEAHGEEQGRTLFRRYADAFPTAYREEFNAEAAVFDIERIEKATAQGTLGINLYRPLE 571
             L    G E           +   AY+  F    A  D+  I   TA   + I+ Y   +
Sbjct: 493  LLARKEGTEI----------SVGEAYQAAFTPAEAYADLGDIAACTAGDPIRISFYHRHQ 542

Query: 572  AEGDELHVKIYHEGRPVPLSDVLPMLEHMDLKVITEAPFEIAIAGHA---APVWIHDFTA 628
               D L +KI+H   PV LS  +P+LE++  +VI+E  ++I +  H      V +HD   
Sbjct: 543  ERPDTLELKIFHADTPVSLSRRVPLLENLGFRVISEQTYDIGVHVHGDEPREVVLHDMEL 602

Query: 629  RSQNGLPIDCAMVKEKFQDAFAAVWDGRMEDDGFNRLVLRAGLTAREVTVLRAYAKYLRQ 688
              ++G  ++ A +    ++AF A W+G  EDD FNRLVL AGLTARE+TVLRAYA+YLRQ
Sbjct: 603  IHRDGHTLNLARIGPALEEAFLAAWNGTTEDDNFNRLVLLAGLTAREITVLRAYARYLRQ 662

Query: 689  ARIPYGQDVVESTLAGHPAIARKLVALFHSRFDPAR----RSQNDPGLAAEIERALDGVK 744
            A I Y Q  +  TL  +P IA  +  LF +R DP      R++    L   IE AL  V 
Sbjct: 663  AGITYSQGYIADTLNKYPTIAADIFRLFSTRMDPTTEVKARTKKCSALLTGIEEALSAVP 722

Query: 745  NLDEDRILRRFLNLLCNTLRTNAYQNGADGRPKTYLSFKIDSRNIDDLPLPRPMVEVFVY 804
            +LDEDRILRR++N + +TLRTN +Q  A+GRP+  L+FK+D + ++ LP PRP  E+FVY
Sbjct: 723  SLDEDRILRRYVNAVQSTLRTNYFQKDAEGRPRAVLAFKLDPKQLEGLPEPRPFREIFVY 782

Query: 805  SPRMEGVHLRGGKVARGGIRWSDRREDFRTEILGLMKAQMVKNTVIVPVGSKGGFVVKRP 864
               +EGVHLR GKVARGG+RWSDR +D+RTE+LGL+KAQ VKN VIVPVG+KGGF  K+ 
Sbjct: 783  GTEVEGVHLRFGKVARGGLRWSDRAQDYRTEVLGLVKAQQVKNAVIVPVGAKGGFYPKQL 842

Query: 865  PPPSAGREAQLAEGIECYKTLMRGLLDITDNLDAQGAVVPPPEVVRHDGDDPYLVVAADK 924
            P     R+     G E YKT +R LL +TDN+  Q  VVPP + +R DGDDPY VVAADK
Sbjct: 843  PV-GGSRDEIFKAGTEAYKTYIRTLLSVTDNIIGQ-EVVPPEDTLRLDGDDPYFVVAADK 900

Query: 925  GTATFSDIANSVSVDHGFWLGDAFASGGSAGYDHKKMGITARGAWESVKRHFRELGHDTQ 984
            GTATFSD AN+++ +  FWL DAFASGGSAGYDHKKMGIT RGAWE+VKRHFRE+  D Q
Sbjct: 901  GTATFSDTANALAQEADFWLDDAFASGGSAGYDHKKMGITGRGAWEAVKRHFREMDVDIQ 960

Query: 985  TQDFTVVGVGDMSGDVFGNGMLLSKHIRLLAAFDHRHIFIDPDPDAARSWEERQRLFDLP 1044
            T  FTV GVGDMSGDVFGNGMLLS+ IRL+AAFDHR IFIDP+PD   S+ ER+R+F LP
Sbjct: 961  TTPFTVAGVGDMSGDVFGNGMLLSEKIRLIAAFDHRDIFIDPEPDIDLSFGERKRMFALP 1020

Query: 1045 RSSWADYDASLLSAGGRVFDRSAKSLELTPEIRQRFGIAKDHVTPLELMQTLLKAEVDLL 1104
            RSSW DYD   LS G  +  RS K + LTPE     GI K   TP E+M  +LK+ VDLL
Sbjct: 1021 RSSWQDYDRKALSPGAMIISRSEKLVTLTPEAMAAIGIDKPKATPFEIMSAILKSPVDLL 1080

Query: 1105 WFGGIGTYLKAAEETNAEVGDKANDALRIDGRDVRAKVIGEGANLGVTQRGRIEAAQHGV 1164
            WFGGIGTY++ A ET+AEVGD+ANDA+R+   DVRA+VIGEGANLGVTQ+GRI  + +G 
Sbjct: 1081 WFGGIGTYVRGANETDAEVGDRANDAIRVSAEDVRARVIGEGANLGVTQKGRIGFSLNGG 1140

Query: 1165 RLNTDAIDNSAGVDTSDHEVNIKILLNDVVVRGDMTLKQRDQLLAAMTDEVAGLVLADNY 1224
            R N+DAIDNSAGV++SD EVNIKI L   +    +T  +R+ LLA+MTDEV  LVL +NY
Sbjct: 1141 RCNSDAIDNSAGVNSSDVEVNIKIALASAMRDDRLTRPKRNTLLASMTDEVGHLVLRNNY 1200

Query: 1225 LQSQALTVARAQGPDALEAQARLIRSLEKAGRLNRAIEYLPDEEELSARMANREGLTRPE 1284
             QS A+++   QG       ARL+  LE  G LNR +E LP ++ +S R      LTRPE
Sbjct: 1201 QQSLAISLTEMQGLANRTPLARLMARLEADGHLNRKVETLPTDQAMSERYQAGRPLTRPE 1260

Query: 1285 LAVLLAYAKITLYDDLLASDLPDDPFMADDLTRYFPKPLRKAHAEAVGRHRLRREIIATS 1344
            + VLL+YAK+ L+D+L+ S++PDDP+    L RYFP  +RKA+A  +  HRLRREIIAT 
Sbjct: 1261 IGVLLSYAKLVLFDELIVSEIPDDPYFTATLERYFPAKMRKAYAGDIHGHRLRREIIATV 1320

Query: 1345 VTNSLVNRTGPTFVKEMMEKTGMGPADVARAYTIVRDAFGLRSLWTGIEDLDTVVPAALQ 1404
            + N  +NR GP FV  + + TG   ADV +A  +  D F L  ++  I+ LD  +  A+Q
Sbjct: 1321 LANETINRGGPAFVSTLTDATGFLSADVVKAAVLALDGFDLPRIYGEIDALDNRISGAIQ 1380

Query: 1405 TSMILETVRHMERAAAWFLASCQQPLDIARETEAFRPGIETLLAGLDNVLDAEETARLTA 1464
              +  E  R     A   L +      +A      R G++ L   +   +  E       
Sbjct: 1381 NRLYHEVGRIFALVAERALRTRASEGSVAEAVARLRDGLQKLRGTMRAAISREGAEEARL 1440

Query: 1465 RVASYQEQGVPAELARRMAALPVLAAAPDLVRIAGRTGRGVADVAAVYFMLGRRFGLEWL 1524
            R A + E GV A+LA+ +A L ++   P++++IA  TG  ++  A  YF +     +  L
Sbjct: 1441 RAAGFIENGVSAKLAKEIAELSLMTLVPEIMQIATVTGEPLSRTAQAYFTVTESLRINRL 1500

Query: 1525 RDKAAAAKAENHWQKQAVAALVDDLFAHQTALTTRVLEAVDQLPAEAPVEAWIAHRRPVV 1584
               A    A   ++  A++  V D+   +  +T   L  V+      PV AW    R  V
Sbjct: 1501 LAAADRVPATEQFESMALSRAVGDIGTARRDITIAAL--VEHKGDRNPVLAWQDRDRQRV 1558

Query: 1585 ERVEQLLSELRTQPNVDLSMLAVANRQLRGLTAG 1618
              V   L  L  +    L+ + VA   L  L  G
Sbjct: 1559 ATVGDQLRLLTEKGETTLAKVTVAAGLLSDLARG 1592


Lambda     K      H
   0.320    0.136    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 5548
Number of extensions: 246
Number of successful extensions: 13
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1618
Length of database: 1595
Length adjustment: 51
Effective length of query: 1567
Effective length of database: 1544
Effective search space:  2419448
Effective search space used:  2419448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (28.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources