Alignments for a candidate for citM in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for citM in Pseudomonas fluorescens FW300-N1B4

Align [Citrate]•M2+ (Ca2+ preferring):H+ symporter, CitH (transports Ca2+, Ba2+ & Sr2+) (characterized)
to candidate Pf1N1B4_1898 Uncharacterized transporter, similarity to citrate transporter

Query= TCDB::P42308
         (426 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1898
          Length = 435

 Score =  555 bits (1431), Expect = e-163
 Identities = 264/428 (61%), Positives = 346/428 (80%), Gaps = 5/428 (1%)

Query: 1   MLAILGFVMMIVFMYLIMSNRLSALIALIVVPIVFALISGFGKDLGEMMIQGVTDLAPTG 60
           ML  LGF M+I FM+LIM+ RLSALIALI++PI+FAL  GF   +G MM++G+T LAPTG
Sbjct: 1   MLTFLGFAMVITFMFLIMTKRLSALIALIIIPIIFALFGGFSPKIGPMMLEGITKLAPTG 60

Query: 61  IMLLFAILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMI 120
           +ML+FAILYF +MIDSGLFDP + KIL  VKGDPLK++VGTAVL + +S+DGDG TTYMI
Sbjct: 61  VMLMFAILYFALMIDSGLFDPAVRKILKLVKGDPLKVSVGTAVLALIVSMDGDGATTYMI 120

Query: 121 TIAAMLPLYKRLGMNRLVLAGIAMLGSGVMNIIPWGGPTARVLASLKLDTSEVFTPLIPA 180
            +AAMLPLY R+GM+  ++AG+ +L  GVMN+ PWGGPTAR  ++L +D S++F P+IPA
Sbjct: 121 CVAAMLPLYSRIGMSPRIMAGLIILAGGVMNMTPWGGPTARAASALHVDPSDIFVPMIPA 180

Query: 181 MIAGILWVIAVAYILGKKERKRLGVI-----SIDHAPSSDPEAAPLKRPALQWFNLLLTV 235
           M+AG++ ++A+AY  GK+ER RLG +      +DH+  S  +    +RP L WFN  LT+
Sbjct: 181 MLAGVVAILAIAYFYGKRERARLGELHLVGDEVDHSEISVSQFPDARRPKLIWFNGALTL 240

Query: 236 ALMAALITSLLPLPVLFMTAFAVALMVNYPNVKEQQKRISAHAGNALNVVSMVFAAGIFT 295
            LM  L+  LLPLPVLFM AF++A++VNYP +++Q+ R++AHAG+ L VV ++FAAGIFT
Sbjct: 241 GLMCTLVAGLLPLPVLFMVAFSIAMIVNYPCLQQQKDRVAAHAGSVLAVVGLIFAAGIFT 300

Query: 296 GILSGTKMVDAMAHSLVSLIPDAMGPHLPLITAIVSMPFTFFMSNDAFYFGVLPIIAEAA 355
           GILSGT MVDAM+ SL+++IPD +GP+L +ITA+VSMPFTFFMSNDAFY+GVLP++AEAA
Sbjct: 301 GILSGTGMVDAMSKSLLAVIPDFLGPYLAVITALVSMPFTFFMSNDAFYYGVLPVLAEAA 360

Query: 356 SAYGIDAAEIGRASLLGQPVHLLSPLVPSTYLLVGMAGVSFGDHQKFTIKWAVGTTIVMT 415
           S YGI A E+ RAS++GQPVHLLSPLVPSTYLLV +AG+ FGDHQ+FT+KWAV   + + 
Sbjct: 361 SHYGITAVEMARASIVGQPVHLLSPLVPSTYLLVALAGIEFGDHQRFTLKWAVLVCLCIL 420

Query: 416 IAALLIGI 423
           +AALL+GI
Sbjct: 421 VAALLMGI 428



 Score = 24.6 bits (52), Expect = 0.006
 Identities = 45/204 (22%), Positives = 83/204 (40%), Gaps = 25/204 (12%)

Query: 67  ILYFGIMIDSGLFDPLIAKILSFVKGDPLKIAVGTAVLTMTISLDGDGTTTYMITIAAML 126
           +++F   +  GL   L+A +L       +  ++   V    +    D    +  ++ A++
Sbjct: 231 LIWFNGALTLGLMCTLVAGLLPLPVLFMVAFSIAMIVNYPCLQQQKDRVAAHAGSVLAVV 290

Query: 127 PLYKRLGMNRLVLAGIAM---LGSGVMNIIP-WGGPTARVLASLKLDTSEVFTPLIP--A 180
            L    G+   +L+G  M   +   ++ +IP + GP   V+ +L    S  FT  +   A
Sbjct: 291 GLIFAAGIFTGILSGTGMVDAMSKSLLAVIPDFLGPYLAVITAL---VSMPFTFFMSNDA 347

Query: 181 MIAGILWVIAVA---YILGKKERKRLGVIS------IDHAPSS-------DPEAAPLKRP 224
              G+L V+A A   Y +   E  R  ++           PS+         E    +R 
Sbjct: 348 FYYGVLPVLAEAASHYGITAVEMARASIVGQPVHLLSPLVPSTYLLVALAGIEFGDHQRF 407

Query: 225 ALQWFNLLLTVALMAALITSLLPL 248
            L+W  L+    L+AAL+  + PL
Sbjct: 408 TLKWAVLVCLCILVAALLMGIFPL 431


Lambda     K      H
   0.328    0.142    0.411 

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: 742
Number of extensions: 29
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 426
Length of database: 435
Length adjustment: 32
Effective length of query: 394
Effective length of database: 403
Effective search space:   158782
Effective search space used:   158782
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: 51 (24.3 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)
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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