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

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.

Downloads

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

Related tools

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