Alignments for a candidate for Psest_0084 in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for Psest_0084 in Sinorhizobium meliloti 1021

Align alpha-ketoglutarate TRAP transporter, 4TM/12TM components (characterized)
to candidate SM_b20291 SM_b20291 hypothetical protein

Query= reanno::psRCH2:GFF84
         (674 letters)



>FitnessBrowser__Smeli:SM_b20291
          Length = 827

 Score =  364 bits (935), Expect = e-105
 Identities = 225/654 (34%), Positives = 345/654 (52%), Gaps = 80/654 (12%)

Query: 44  RAGHVGFLLLLVFLCYPA-RGNGKPFQPVA-WLLGLAGFATFFYQWYFEADLIQRSGDMT 101
           RA H+GF L L FL YPA + + +   P+A W+LG  G     Y + F  +L  R G  +
Sbjct: 29  RAIHLGFALFLTFLAYPALKSSPRDRVPLADWVLGALGAFAGAYLFLFYGELAGRPGQPS 88

Query: 102 TADMVVGLTLIVLVFEAARRVMGIALPIICALFLAYGLLGEYLPGDLAHRGYYLDQIVNQ 161
           T D+V G   I+L+ EA RR +G+ +  +  +F+ Y   G+Y+P  + HRG  L + +N 
Sbjct: 89  TLDLVTGTAGILLLLEATRRALGLPMVFVAGVFIFYTFAGQYMPDVIQHRGASLVKFINH 148

Query: 162 LSFGTEGLYGTPTYVSATYIFLFILFGSFLEQAGMIKLFTDFAMGLFGHKLGGPAKVSVV 221
               TEG++G    VS +++FLF+LFG+ LE+AG        ++ L GH  GGPAKV+VV
Sbjct: 149 QWLTTEGVFGIALGVSTSFVFLFVLFGTLLEKAGAGNWMMQISIALLGHLRGGPAKVAVV 208

Query: 222 SSALMGTITGSGVANVVTTGQFTIPLMKRFGYRPAFAGGVEATSSMGSQIMPPVMGAVAF 281
           SSAL G ++GS V+NVV+ G FTIPLMKR G     AG +EA++S+  QIMPPVMGA AF
Sbjct: 209 SSALNGVVSGSSVSNVVSGGIFTIPLMKRTGLSGVKAGAIEASASINGQIMPPVMGAAAF 268

Query: 282 IMAETINVPFVEIAKAALIPALLYFGSVFWMVHLEAKRAGLKGLPKDECPSAMAAVKERW 341
           +M E + +P+ EI K AL+PA+  + ++ +MVHLEA +  ++ +P+   P     ++ERW
Sbjct: 269 LMVEYVGIPYSEIVKHALLPAVFSYIALLYMVHLEAVKLNMQPIPQRPTP-----MRERW 323

Query: 342 Y--------------LLIPLVVLVWLLFSGRTPMFAGTIGLALTAIVILGS--------- 378
                          LL   ++ +   F    P+     G+AL    I  S         
Sbjct: 324 LRMGLGLAGSVLAICLLYYGIIAIRAAFGESAPLLLAIAGVALYIATIWYSSRYPDLELD 383

Query: 379 ---AIILKVS----------NFALRI-----------------AFWIALGLLCAGFFQLG 408
              A IL++           +F + I                 AFW  L ++     +  
Sbjct: 384 DPDAPILELPRAWDVTRTGLDFLIPIVVLLWCLMVEQLSPGLSAFWATLTIIAIVATRKP 443

Query: 409 IGVIF---GVIAALVAVCWFIKGGRDTLVICLHALVEGARHAVPVGIACALVGVIIGVVS 465
           +  IF    V  ++ A  W +  G          L  GAR+ + + +A A  G+++G ++
Sbjct: 444 LMAIFRKEDVAGSVRAAAWDLTDG----------LALGARNMIGIAVATATAGIVVGTIT 493

Query: 466 LTGVASTFAGYILAVGENNLFLSLLLTMLTCLVLGMGIPTIPNYIITSSIAAPALLDLG- 524
           LTG+       +  +   N+ + L+L     LVLGMGIPT  NYI+ +++ AP +++LG 
Sbjct: 494 LTGLGLMMTELVEFISGGNVIMMLILIAAISLVLGMGIPTTANYILVATLMAPVVVELGS 553

Query: 525 -----VPLIVSHMFVFYFGIMADLTPPVALACFAAAPIAKERGLKISMWAIRIAIAGFIV 579
                +PLI  H+FVFYFGIMAD+TPPV LA FAAA I+KE  +         ++   I+
Sbjct: 554 QAGLAIPLIAVHLFVFYFGIMADITPPVGLAAFAAAAISKEDPIATGFQGALYSLRTAIL 613

Query: 580 PFMAVYNPALMMQGGD-WGATLYMLFKAAFAVGLWGAVFTGYLQRPMALWEKVL 632
           PF+ ++NPA+++ G D W  T+++   +  A+ ++ A    +      LWE  +
Sbjct: 614 PFVFIFNPAILLIGVDTWAHTIWVAAISLAAILIFSAATMNWFVTKSRLWESAV 667


Lambda     K      H
   0.330    0.143    0.445 

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: 1593
Number of extensions: 89
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 2
Length of query: 674
Length of database: 827
Length adjustment: 40
Effective length of query: 634
Effective length of database: 787
Effective search space:   498958
Effective search space used:   498958
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 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 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:

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