Alignments for a candidate for rocA in Azohydromonas australica DSM 1124

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Azohydromonas australica DSM 1124

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_156901726.1 H537_RS0114840 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::acidovorax_3H11:Ac3H11_2850
         (1261 letters)



>NCBI__GCF_000430725.1:WP_156901726.1
          Length = 1254

 Score =  879 bits (2272), Expect = 0.0
 Identities = 535/1283 (41%), Positives = 732/1283 (57%), Gaps = 90/1283 (7%)

Query: 21   LRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQLALRIAKALRERKASAGRAG 80
            L + + A I AA    E  A+A L+ +A L   Q +  + LA R+A+ +R+ +  AG   
Sbjct: 14   LLSTLRARIDAADLVDEATAVAALMKEAALQPAQLSTTQALAARLAQGVRKSRLDAGGID 73

Query: 81   IVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIRDKISHGQWDAHLGKSPSLFV 140
            +   L QEFSL S+EGVALMCLAEA+LR+PD  TR+ LIRDKI    W AH G SPSLFV
Sbjct: 74   L---LTQEFSLDSREGVALMCLAEAMLRVPDTETRNKLIRDKIVDQDWRAHAGNSPSLFV 130

Query: 141  NAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRKGVDMAMRMMGEQFVTGETID 200
            NA  WGL +TGKL+    E +L  +LS ++ KGGE ++R GV  AMR++G+QFVTG+TI+
Sbjct: 131  NATAWGLFVTGKLLKKPDEQALAAALSNVLRKGGEGVVRAGVAYAMRLLGKQFVTGQTIE 190

Query: 201  EALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQAIHAIGKASAGRGIYEGPGI 260
            EA+  AR+ E  G+RYSYDMLGE ALT EDA  YY +Y   I  IGK + G+G  EGPG+
Sbjct: 191  EAIAEARSREKRGYRYSYDMLGEGALTPEDADAYYEAYLHTIEEIGKTAKGQGPIEGPGV 250

Query: 261  SIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIGLNIDAEETDRLELSLDLLER 320
            S+KL+ LHPRY  +Q GRV++E+YP +L+L   A++YDIG ++D EE+ R  L+L++L+R
Sbjct: 251  SVKLTGLHPRYEVSQHGRVIEEMYPRLLKLACAARRYDIGFHLDQEESARFPLTLEMLQR 310

Query: 321  LCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQRRLMVRLVKGAYWDSEIKRAQ 380
            L H P L GW+G+G  +QAYQKR   V+D +++L R TQRR++VRLVKGAYWD+EIKR Q
Sbjct: 311  LAHAPELQGWSGLGISLQAYQKRGRAVVDWLIELGRSTQRRILVRLVKGAYWDTEIKRCQ 370

Query: 381  VDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFATHNAETVATIYQLAGSNYYAG 440
             +G  +YPV+TRKVH+D+SY+ACAK LLAA +A++PQFATHNA ++A ++ LAG      
Sbjct: 371  AEGTANYPVFTRKVHSDVSYLACAKALLAAQDAIFPQFATHNAFSIAAVHTLAGDK---- 426

Query: 441  QYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPCRIYAPVGTHETLLAYLVRRL 500
             YEFQCLHGMGE +Y+Q+V            G   LGR CRIYAPVG H TLLAYLVRRL
Sbjct: 427  AYEFQCLHGMGESIYDQIV------------GPSNLGRACRIYAPVGPHATLLAYLVRRL 474

Query: 501  LENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGTAGLPHPRIPLPAALYGAHRS 560
            LENGANTSFVN++ D  + ++++V  PV      A    T G P+P IPLP  L  + R 
Sbjct: 475  LENGANTSFVNQVVDTDVRIEDIVADPV------AKAAQTRGQPNPGIPLPPHL-PSWRK 527

Query: 561  NSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPAGTTQP--VRNPADHNDVVGQ 618
             S  + LS+      L A  +          PL A    A   QP  V NPA  N+ VG 
Sbjct: 528  GSAVVALSDR---AALQAEYRRLMESRPAIEPLCAFASSAAAQQPVVVLNPAARNEQVGT 584

Query: 619  VQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLLEERIQPLMGLLMREAGKS 678
               +  ADV QAL  +Q    +W +   +ER   +   A  +E     L  LL+ E GK+
Sbjct: 585  YTSSGVADVAQALRTSQEGQKAWGSRSLSERMQMITAAAQAMESSAARLGALLVLECGKT 644

Query: 679  ASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISPWNFPLAIFMGQVAAALAA 738
             + A  E+R   D  R Y AQ  +         LG VA ++  + PL    GQ+AAAL A
Sbjct: 645  PAEAAEEIRRVTDLCRLYVAQAATDPTVTAAKSLGTVAVVTSSSAPLYTLAGQIAAALLA 704

Query: 739  GNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGETVGARLIGDARVMGVMFTG 798
            GN V+AKP+    L+A EAV+    AGVP  A+QLL G G TVGA L+ D  V  V+FTG
Sbjct: 705  GNAVVAKPSSHASLVAHEAVKAFHAAGVPANALQLLLGAGGTVGAALVRDPGVAAVLFTG 764

Query: 799  STEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSALVEQVVGDAVSSAFDSAGQ 858
            + + A  ++  V+    A      L+A TGG NAMIVDSSAL EQV+ DAV  A+D AGQ
Sbjct: 765  TPKTAADIREAVSTLPHAPA----LMANTGGFNAMIVDSSALPEQVISDAVFGAYDCAGQ 820

Query: 859  RCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVGPVIDAEAQAGIAQHIEKF 918
            + ++L++LC+Q+  AD+++ ML   + E  VG+P E   DVGPV     Q     ++ + 
Sbjct: 821  KGASLKLLCLQDSVADKIIGMLGAMLLERSVGDPREPDTDVGPVATQAIQDQADAYLARM 880

Query: 919  KAQGHRVFQHPNHVSAISAPGTFVPPTLI---ELNHIGELQREVFGPVLHLVRYARSDLD 975
            +A+G RV +   H    S  G +V P ++   ++  + ++ + V GP+LH+VR+   +L+
Sbjct: 881  EAKGLRVIRTTRHHG--STQGLYVQPAIVDVGDMQALAQIDQNVRGPILHVVRWKAHELE 938

Query: 976  QLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVGAVVGVQPFGGEGLSG 1035
             LL Q+N      T G+HTRI+ET  +V+ ++ A  ++VNR +  A VG+Q  GG G +G
Sbjct: 939  ALLAQLNTQADVATLGLHTRINETTGQVLTQSTAEAIFVNRAIHTARVGMQVEGGMGHAG 998

Query: 1036 TGPKAGGPLYLLRLLSQRPADALART---------------FAEADRTSPHDTERRERHL 1080
            TGP   G L+L RL+  +P   LA +               F E         E R +HL
Sbjct: 999  TGPSISGSLFLSRLV--QPLHVLATSNEGPFAPRRNLSSAKFMEYPVAKGESLEERNQHL 1056

Query: 1081 APLATLQQWAHNQGNLALAGHCQR--------------FAQETQSGTSRTLPGPTGERNV 1126
                T++Q A     LA      R                   Q    R LP  +GE N 
Sbjct: 1057 R--RTIEQRATLLRRLAAGTAAARPGLLPAPQQAQLDALQSVAQQCLPRGLPALSGEENT 1114

Query: 1127 YTLAPRARVLCLAHSVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVM-LQDN 1185
                PR   LC+  ++DD + Q    +A G + + P           T V AQV+  +  
Sbjct: 1115 LEYLPRGAALCMGPTMDDFVAQAMTAVAVGASVMLPRTG-------ETSVLAQVLGAEQC 1167

Query: 1186 TLSD-------GSVALDAVLHHGDAPSLQAVCTTLARRPGPIVGVTALQPGAADI-PLER 1237
            TL D         +   AVL        QA+   +A    P+  V  +  G   +    R
Sbjct: 1168 TLFDAMRESLSSPLKPAAVLSAYSGEQAQALRKRVA-ASWPLAFVELVTRGPDGLYDWTR 1226

Query: 1238 LLIERALSVNTAAAGGNASLMTI 1260
            L+ ER  S+N +AAGG+ +LM +
Sbjct: 1227 LVRERMTSINVSAAGGSEALMMV 1249


Lambda     K      H
   0.318    0.133    0.387 

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: 3342
Number of extensions: 156
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1261
Length of database: 1254
Length adjustment: 48
Effective length of query: 1213
Effective length of database: 1206
Effective search space:  1462878
Effective search space used:  1462878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 bits)

This GapMind analysis is from Apr 09 2024. 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)
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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 2024 update 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