GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Echvi_1880 in Alkalitalea saponilacus SC/BZ-SP2

Align SSS sodium solute transporter (characterized, see rationale)
to candidate WP_079555937.1 CDL62_RS06475 sodium/solute symporter

Query= uniprot:L0FZT5
         (624 letters)



>NCBI__GCF_002201795.1:WP_079555937.1
          Length = 631

 Score =  673 bits (1736), Expect = 0.0
 Identities = 354/641 (55%), Positives = 456/641 (71%), Gaps = 28/641 (4%)

Query: 1   MSAGFSTLDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAA 60
           M+AGF+T+DY+IF  YA  I+ +GLW+SRTKKG EK +++YFLA  +L+WWA+GASL+AA
Sbjct: 1   MNAGFTTIDYLIFGAYAALIMGIGLWISRTKKGEEKDSKDYFLAGGTLSWWAIGASLIAA 60

Query: 61  NISAEHFIGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFN 120
           NISAEHFI  SGSG+AIGLG++AYEWIAAI LI+VAKY LP  L   ++TMPQF  ER+ 
Sbjct: 61  NISAEHFIAMSGSGYAIGLGMAAYEWIAAIVLILVAKYLLPQMLDKKIFTMPQFARERYG 120

Query: 121 KGVSTAFAVFWLLVYVFVNLTSVSYLGALALDKIMGIPLQYGIIGLLIFSGIYSIYGGLE 180
            GVS  F+ FWLLVYVFVNLTSV++LGALA+++I+G+P+ YG+ GLLIF+G+YSIYGG++
Sbjct: 121 SGVSFFFSFFWLLVYVFVNLTSVAWLGALAMNQILGVPILYGVPGLLIFAGVYSIYGGMK 180

Query: 181 AVAWTDVVQVIILVAGGLITTFLALDAV-GMGDGIFAGMSNLYN-----DAKDHFVMIMP 234
           +VAWTD+VQV  L+ GGLIT + ALDAV G G   F G   + N     +   HF MI+ 
Sbjct: 181 SVAWTDIVQVFFLIFGGLITAWFALDAVAGDGKSAFEGFRVVLNQIRASETDTHFNMIIG 240

Query: 235 QGRVMVPDGLGGSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKG 294
                      G+RD+F +LPGLAVI G MWLTN+GYWGFNQ+IIQKGLAAK+++EAK+G
Sbjct: 241 DSE--------GTRDSFLNLPGLAVIFGAMWLTNIGYWGFNQFIIQKGLAAKNLKEAKRG 292

Query: 295 LLFAGYLKLLMPIIVVIPGIAAYVLIN---DYSPEQLAAILNMPVEHI--GTIQKSDEAY 349
           LLFA YLK+L+PIIV+IPGI AYV+     + +   LA I  M    +  G +  SD+AY
Sbjct: 293 LLFAAYLKILIPIIVIIPGITAYVIHGMSVETADGSLAFINQMGDSTLLAGEVAISDDAY 352

Query: 350 PWLLRNFIPNGIRGLAFAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRT 409
           PWLLRNF P GIRGLAFAAL AA++SSLAS++NSTSTIFT+DIYK     +A+  QLVR 
Sbjct: 353 PWLLRNFAPVGIRGLAFAALVAAVISSLASLLNSTSTIFTLDIYKTLINKSASERQLVRV 412

Query: 410 GRIVAVVALAIAMIVA-PQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAAL 468
           GR  A VALAIA++ A P L  LDQ FQYIQEYTG+IYPGVV VFGMG++W++AT  AAL
Sbjct: 413 GRFAAFVALAIAIVAARPLLGGLDQAFQYIQEYTGFIYPGVVAVFGMGILWKRATNRAAL 472

Query: 469 WTAIATIPAGIVFKIFYPEMPFLLRMGYVFIILCFIASLISFAEKKKF-ANPDYKTNKQA 527
           WT IATIP GI+ K+  P++P+++RMGYVFIIL  ++  +   +K K  A P   + +  
Sbjct: 473 WTTIATIPTGILMKLALPDLPWMIRMGYVFIILVGLSITLVLTDKHKVKATP--MSPENI 530

Query: 528 AKTVASSYFFIILGIICAVLGFA----LFN-SYEHVGIESIFMIAALFLMLGTILYTNVK 582
            K + + + F  L II  V G      LF     H+G  SIFM  A+   L  I+YTN K
Sbjct: 531 KKQMNAGHVFAALAIITFVAGMLWGTNLFGMGMLHLGFNSIFMTTAMMTFLAVIMYTNAK 590

Query: 583 METADPKSFNTDPVLFNTTSSFNLGAAGIILIVGLLYYFFW 623
               D K+++ +P +  T   F   A GI++I+  LY +FW
Sbjct: 591 SSLQDDKAYDFNPDIIKTDKVFFTMAMGIVVIIVALYAYFW 631


Lambda     K      H
   0.327    0.142    0.427 

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: 1359
Number of extensions: 66
Number of successful extensions: 5
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: 624
Length of database: 631
Length adjustment: 38
Effective length of query: 586
Effective length of database: 593
Effective search space:   347498
Effective search space used:   347498
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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